Validated Unbiased for Microbiome Measurements: Unbiased cellular lysis validated using the ZymoBIOMICS Microbial Community Standard.

Transcription

1 90 INSTRUCTION MANUAL ZymoBIOMICS DNA Miniprep Kit Catalog Nos. D4300T, D4300, & D4304 Highlights Validated Unbiased for Microbiome Measurements: Unbiased cellular lysis validated using the ZymoBIOMICS Microbial Community Standard. Inhibitor-Free DNA from Any Sample: Isolate ultra-pure DNA ready for any downstream application. Certified Low Bioburden: Boost your detection limit for low abundance microbes. Simple Workflow: Simply bead-beat sample, purify via spin-column, and filter to remove PCR inhibitors. No precipitation or lengthy incubations! Contents Product Contents & Specifications... 1 Product Description Protocol Appendices A. Sample Collection... 6 B. Application Notes C. Standardize Sample Preparation with ZymoBIOMICS Microbial Standards D. Troubleshooting Ordering Information For Research Use Only Ver

2 Page 1 Satisfaction of all Zymo Research products is guaranteed. If you should be dissatisfied with this product please call Product Contents ZymoBIOMICS DNA Miniprep Kit (Kit Size) D4300T (5 preps.) D4300 (50 Preps.) D4304 (50 Preps.) ZR BashingBead Lysis Tubes (0.1 & 0.5 mm) ZymoBIOMICS Lysis Solution 4 ml 40 ml - ZymoBIOMICS DNA Binding Buffer 1 6 ml 100 ml 100 ml ZymoBIOMICS DNA Wash Buffer 1 2 ml 50 ml 50 ml ZymoBIOMICS DNA Wash Buffer 2 5 ml 60 ml 60 ml ZymoBIOMICS DNase/RNase Free Water 1 ml 10 ml 10 ml ZymoBIOMICS HRC Prep Solution 3 ml 30 ml 30 ml Zymo-Spin III-F Filters Zymo-Spin III-HRC Filters Zymo-Spin IIC-Z Columns Collection Tubes Instruction Manual Storage Temperature - Store all kit components (i.e., buffers, columns) at room temperature. Note - Integrity of kit components is guaranteed for up to one year from date of purchase. Reagents are routinely tested on a lot-to-lot basis to ensure they provide maximal performance and reliability. Specifications 1 See endospore lysis efficiency data in Appendix B. 2 This equates to approximately 10 9 bacterial cells and 10 8 yeast cells. 3 For water samples, filter using desired filter (not provided). Cut the filter into small pieces and place into ZR BashingBead Lysis Tube (0.1 & 0.5 mm). Alternatively, up to 250 µl water can be processed directly. 4 DNA/RNA Shield provides an accurate molecular signature of the sample at the time of collection by preserving nucleic acids at ambient temperature and inactivating organisms including infectious agents (see Appendix A). Sample Sources Bacterial (including endospores) 1, fungal, protozoan, algal, viral, mitochondrial, and host DNA is efficiently isolated from 200 mg of mammalian feces, 250 mg soil, and mg (wet weight) of bacterial/fungal cells 2, biofilms, and water 3. Bead Beating System The innovative ZymoBIOMICS lysis system enables complete homogenization/disruption of the microbial cells walls and accurate microbial DNA analysis, free of bias. To ensure unbiased lysis, calibration of each bead-beating device is recommended by using the ZymoBIOMICS Microbial Community Standard (see Appendix C). DNA Purity High quality, inhibitor-free DNA is eluted with ZymoBIOMICS DNase/RNase Free Water and is suitable for all downstream applications including PCR and Next-Generation Sequencing. DNA Integrity On average, post bead beating, genomic DNA is between kb depending on the initial quality of the sample, making it amenable to Next-Generation Sequencing platforms requiring high molecular weight DNA. For optimal DNA integrity, collect samples in DNA/RNA Shield 4. DNA Recovery Up to 25 µg total DNA can be eluted into 100 µl (50 µl minimum). Bioburden A single preparation is guaranteed to contain less than 3 bacterial genomic copies per µl of eluate as determined by quantitative amplification of the 16S rrna gene when eluted using 100 µl water. Equipment Microcentrifuge, vortex/disruptor Genie, high speed cell disrupter (recommended).

3 Page 2 Product Description The ZymoBIOMICS DNA Miniprep Kit is designed for purifying DNA from a wide array of sample inputs (e.g. feces, soil, water, biofilms, etc.), that is immediately ready for microbiome or metagenome analyses. The ZymoBIOMICS innovative lysis system eliminates bias associated with unequal lysis efficiencies 1 of different organisms (e.g. Gram-negative/positive bacteria including endospores 2, fungi, protozoans, algae, etc.), making it ideal for microbial community profiling. Unbiased mechanical lysis of tough microbes is achieved by bead beating with the innovative ultra-high density BashingBeads and validated using the ZymoBIOMICS Microbial Community Standard 3, as shown in Figure 3. In addition, the ZymoBIOMICS DNA Miniprep Kit is equipped with Zymo Research s proprietary OneStep PCR Inhibitor Removal technology enabling PCR from the most PCR prohibitive environmental samples rich in humic and fulvic acids, tannins, melanin, and other polyphenolic compounds. Coupling state-of-the-art lysis technology with Zymo-Spin Technology results in superior yields of ultra-pure DNA ideal for all downstream applications including PCR, arrays, 16S rrna gene sequencing, and shotgun sequencing 4. Innovation. Pure & Simple. 1 Chemical, enzymatic, and inferior lysis matrices (beads) lead to unrealistic representation of organisms in downstream metagenomic analyses that is not reflective of actual abundance. 2 See endospore lysis efficiency data in Appendix B. 3 For more information on the ZymoBIOMICS Microbial Community Standard (D6300) & ZymoBIOMICS Microbial Community DNA Standard (D6305), see Appendix C. Ultra-pure DNA from Inhibitor Rich Samples 4 DNA is predominately kb and amenable to Next-Generation Sequencing techniques requiring high molecular weight DNA. Figure 1. The ZymoBIOMICS DNA Miniprep Kit provides inhibitor-free DNA even when challenged with extremely inhibitor rich samples. Real-time PCR was used to evaluate eluates recovered using the ZymoBIOMICS DNA Miniprep Kit, and kits from Suppliers Q 1, P, and Q 2. Reaction volumes consisted of either 10% or 35% of the eluate from each kit to detect the presence of PCR inhibitors. Each reaction contained 25 ng of Brettanomyces DNA. Delayed and/or no amplification indicates PCR inhibition from inefficient inhibitor removal. Superior Yields Zymo- Supplier L BIOMICS Q 1 P Q 2 Figure 2. The ZymoBIOMICS DNA Miniprep Kit provides superior yields when compared to Suppliers Q 1, P, and Q mg of feces was processed using each kit according to the manufacturers recommended protocol. DNA was eluted using 100 µl ZymoBIOMICS DNase/RNase Free Water. 6 µl of each sample was visualized in a 1.0% (w/v) agarose/ethidium bromide gel. Samples were processed in triplicate. L is a 1Kb ladder. Zymo Research offers a full suite of ZymoBIOMICS Services for reliable, accurate microbial and metagenomic analyses. Services include: Microbial Composition Profiling, Novel Microbe Identification, and Customizable Bioinformatics. For details visit us at: services/metagenomics Or contact us at: services@zymoresearch.com

4 Page 3 A) Bias Free Microbial DNA Extraction Using ZymoBIOMICS DNA Miniprep Kit Validated with the ZymoBIOMICS Microbial Community Standard Theoretical ZymoBIOMICS HMP Protocol Supplier Q 1 Supplier Q 2 DNA Miniprep Kit B) Bias Free Microbial DNA Extraction Using ZymoBIOMICS DNA Miniprep Kit From Human Stool ZymoBIOMICS HMP Protocol Supplier Q 1 Supplier Q 2 DNA Miniprep Kit Figure 3. A) The ZymoBIOMICS DNA Miniprep Kit provides unbiased representation of the organisms extracted from the ZymoBIOMICS Microbial Community Standard. DNA was extracted from ZymoBIOMICS Microbial Community Standard using four different DNA extraction methods (ZymoBIOMICS DNA Miniprep Kit, Human Microbiome Project Protocol, Supplier Q 1, and Supplier Q 2 ) and analyzed using 16S rrna gene sequencing. 16S rrna genes were amplified with primers targeting v3-4 region and the amplicons were sequenced on Illumina MiSeq (2x250bp). Overlapping paired-end reads were assembled into complete amplicon sequences. The composition profile was determined based on sequence counts after mapping amplicon sequences to the known 16S rrna genes of the eight different bacterial species. B) The ZymoBIOMICS DNA Miniprep Kit reliably isolates DNA from even the toughest to lyse Gram positive organisms, enabling unbiased analyses of microbial community compositions. There is a significant increase in yield and Gram-positive bacterial abundance when DNA was isolated using the ZymoBIOMICS DNA Miniprep Kit. Correlated with the results in Figure 3A, it can be concluded that unbiased DNA isolation was achieved. DNA was extracted from 200 µl of human feces suspended in PBS (10 % m/v) using four different DNA extraction methods (ZymoBIOMICS DNA Miniprep Kit, Human Microbiome Project Protocol, Supplier Q 1, and Supplier Q 2 ) and analyzed using 16S rrna gene sequencing. 16S rrna genes were amplified with primers targeting v3-4 region and the amplicons were sequenced on Illumina MiSeq (2x250bp). Overlapping paired-end reads were assembled into complete amplicon sequences. Amplicon sequences were profiled with Qiime using Greengenes 16S rrna gene database (gg_13_8).

5 Page 4 Protocol 1. Add sample to a ZR BashingBead Lysis Tubes (0.1 & 0.5 mm). Add 750 µl ZymoBIOMICS Lysis Solution to the tube and cap tightly. Note: For samples stored and lysed in DNA/RNA Shield Lysis Tubes, do not add ZymoBIOMICS Lysis Solution and proceed to Step 2. Sample Type Maximum Input Feces 200 mg Soil 250 mg Liquid Samples 1 and Swab Collections µl Cells (isotonic buffer, e.g. PBS) mg (wet weight) (10 9 bacterial and 10 8 yeast cells) Samples in DNA/RNA Shield,3 1 ml 2. Secure in a bead beater fitted with a 2 ml tube holder assembly and process at maximum speed for 5 minutes. Note: Processing time will vary based on sample input and bead beater. Times may be as little as 5 minutes when using high-speed cell disrupters (FastPrep -24) or as long as 20 minutes when using lower speeds (e.g., Disruptor Genie ) Centrifuge the ZR BashingBead Lysis Tubes (0.1 & 0.5 mm) in a microcentrifuge at 10,000 x g for 1 minute. 4. Transfer up to 400 µl supernatant to the Zymo-Spin III-F Filter in a Collection Tube and centrifuge at 8,000 x g for 1 minute. Discard the Zymo-Spin III-F Filter. 5. Add 1,200 µl of ZymoBIOMICS DNA Binding Buffer to the filtrate in the Collection Tube from Step 4. Mix well. 6. Transfer 800 µl of the mixture from Step 5 to a Zymo-Spin IIC-Z Column in a Collection Tube and centrifuge at 10,000 x g for 1 minute. For Technical Assistance: or tech@zymoresearch.com 1 For water samples, filter using desired filter (not provided). Cut the filter into small pieces and place into ZR BashingBead Lysis Tubes (0.1 & 0.5 mm). 2 Swabs can also be cut or broken, then placed directly in bead beating tube. For more information on processing swab samples, see Appendix B. 3 Up to 1 ml of sample in DNA/RNA Shield can be processed directly in ZR BashingBead Lysis Tube. Adjust final volume to 1 ml with ZymoBIOMICS Lysis Solution or DNA/RNA Shield, if necessary. 4 For optimal lysis efficiency and unbiased profiling, all bead beater devices beyond those validated by Zymo Research should be calibrated using the ZymoBIOMICS Microbial Community Standard (see Appendix C). 7. Discard the flow through from the Collection Tube and repeat Step Add 400 µl ZymoBIOMICS DNA Wash Buffer 1 to the Zymo-Spin IIC-Z Column in a new Collection Tube and centrifuge at 10,000 x g for 1 minute. Discard the flow-through. 9. Add 700 µl ZymoBIOMICS DNA Wash Buffer 2 to the Zymo-Spin IIC-Z Column in a Collection Tube and centrifuge at 10,000 x g for 1 minute. Discard the flow-through. 10. Add 200 µl ZymoBIOMICS DNA Wash Buffer 2 to the Zymo-Spin IIC-Z Column in a Collection Tube and centrifuge at 10,000 x g for 1 minute.

6 Page 5 For Technical Assistance: or tech@zymoresearch.com 5 In some cases a browncolored pellet may form at the bottom of the tube after centrifugation. Avoid this pellet when collecting the eluted DNA. 6 If fungi or bacterial cultures were processed; the DNA is now suitable for all downstream applications. 11. Transfer the Zymo-Spin IIC-Z Column to a clean 1.5 ml microcentrifuge tube and add 100 µl (50 µl minimum) ZymoBIOMICS DNase/RNase Free Water directly to the column matrix and incubate for 1 minute. Centrifuge at 10,000 x g for 1 minute to elute the DNA 5, Place a Zymo-Spin III-HRC Filter in a new Collection Tube and add 600 µl ZymoBIOMICS HRC Prep Solution. Centrifuge at 8,000 x g for 3 minutes. 13. Transfer the eluted DNA (Step 11) to a prepared Zymo-Spin III-HRC Filter in a clean 1.5 ml microcentrifuge tube and centrifuge at exactly 16,000 x g for 3 minutes. The filtered DNA is now suitable for PCR and other downstream applications.

7 Page 6 Appendix A Sample Collection For high quality reproducible microbiomics data, DNA/RNA Shield is recommended for sample collection to avoid bias or erroneous results due to compositional changes from nucleic acid degradation or microbial growth. DNA/RNA Shield provides an unbiased molecular snapshot of the sample at the time of collection by preserving nucleic acids at ambient temperature and inactivating organisms including infectious agents. Samples can be stored and transported easily and safely with DNA/RNA Shield and is ideal for applications such as PCR, 16S rrna gene sequencing, and shotgun metagenomic sequencing. DNA/RNA Shield can preserve nucleic acids in nearly any sample including feces, soil, saliva, blood, and tissues. DNA/RNA Shield - Lysis Tube (Microbe) Simply add sample, seal and store at ambient temperature. The Lysis Tube is immediately ready for bead beating, thereby streamlining the collection to extraction transition. (Cat. No. R1103) DNA/RNA Shield Fecal Collection Tube The collection device is specifically designed for easy collection and stabilization of feces. Includes a scoop built for collecting 1 gram of feces (or any other sample such as saliva or soil). (Cat. No. R1101) DNA/RNA Shield Swab Collection Tube Easy collection of biological samples; swab has breakable tip to allow for easy sample collection and removes the need to dispose of a potentially biohazardous swab material. (Cat. No. R1106 & R1107) A) DNA/RNA Shield Preserves Nucleic Acids at Room Temperature B) DNA/RNA Shield Preserves Microbial Composition at Room Temperature C) DNA/RNA Shield Inactivates Pathogens for Safe Transport and Storage Figure 4. A) Nucleic acids in stool are effectively stabilized in DNA/RNA Shield at room temperature. Graph shows spike-in DNA and RNA controls from stool purified at the indicated time points and analyzed by (RT)qPCR. Controls: HSV-1 and HIV (AcroMetrix, Life Technologies). B) Microbial composition of stool is unchanged after one month at ambient temperature with DNA/RNA Shield. Stool samples suspended in DNA/RNA Shield and stored at room temperature were compared to stool without preservative for one month. They were sampled at the indicated time points and processed with ZymoBIOMICS DNA Miniprep Kit. The extracted DNA was then subjected to microbial composition profiling via 16S rrna gene targeted sequencing. Graphs show both phylum composition (left) and genus composition (right). Samples stored with DNA/RNA Shield had a constant microbial composition while the samples stored without shifted dramatically. C) Viruses, bacteria and yeast are effectively inactivated by DNA/RNA Shield. Samples containing the infectious agent (viruses, bacteria, yeast) were treated with DNA/RNA Shield or mock (PBS) treated for 5 minutes. Titer (PFU) was subsequently determined by plaque assay. Validated by: Influenza A - D. Poole and Prof. A. Mehle, Department of Medical Microbiology and Immunology, University of Wisconsin, Madison; Ebola (Kikwit) - L. Avena and Dr. A. Griffiths, Department of Virology and Immunology, Texas Biomedical Research Institute; HSV-1/2.

8 Page 7 Appendix B Application Notes DNA/RNA Shield Lysis Tubes (Microbe) (Cat. No. R1103) 1. Collect sample directly into the DNA/RNA Shield Lysis Tube (Microbe). 2. Directly proceed to Step 2 of the protocol (page 4) and bead beat in the DNA/RNA Shield Lysis Tube (Microbe) according to provided recommendations. 3. Proceed with the remaining protocol as written. DNA Viruses For unbiased metagenomics analysis of viruses, incorporating a Proteinase K digestion prior to bead beating is recommended. 1. Following Step 2 (page 4) add 5% (v/v) of Proteinase K (Cat. No. D ) to the lysate within the ZR BashingBead Lysis Tubes (0.1 & 0.5 mm) and incubate for 30 minutes at 55 C. 2. Proceed to Step 3 (page 4) and continue with the remaining protocol as written. Cheese and Protein Rich Biofluids (e.g. Milk, Sputum, Saliva, Spinal Fluid, Blood, and Serum) 1. Add g of cheese or 200 µl of biofluid to the ZR BashingBead Lysis Tubes (0.1 & 0.5 mm). Add 750 µl of ZymoBIOMICS Lysis Solution. 2. Add 2% (v/v) of Proteinase K (Cat. No. D ) to the ZR BashingBead Lysis Tubes (0.1 & 0.5 mm) and incubate for 30 minutes at 55 C. 3. Continue on to Step 2 (page 4) and proceed with the protocol as written. Plant Tissue (Leaves and other plant material) Plant tissues such as leaves and roots contain DNA sources within the host tissue that can overwhelm 16S rrna gene targeted sequencing (from both mitochondria & chloroplast). Microbes must be removed from the plant surface to exclude host tissue from the bead beating process. (A) Plant tissue Centrifugation of cells 1. Suspend plant tissue in isotonic solution (e.g. PBS) and gently sonicate or vortex briefly. 2. Remove plant tissue from solution and centrifuge at 15,000 x g for 10 minutes to pellet the cells. 3. Without disturbing the pellet, slowly decant or pipette out the supernatant, leaving behind µl of pellet. 4. Add ZymoBIOMICS Lysis Solution to the cells to a final volume of 1 ml and mix to resuspend. Transfer the mixture to the ZR BashingBead Lysis Tubes (0.1 & 0.5 mm) and proceed to Step 2 (page 4). (B) Plant tissue Filtration of cells 1. Place plant tissue in a submerging volume of PBS inside of a conical tube and gently sonicate or vortex briefly. Remove plant tissue from liquid volume. 2. Filter liquid using a 0.22 µm filter (not provided). 3. Cut the filter and place directly into the ZR BashingBead Lysis Tubes (0.1 & 0.5 mm) and proceed to Step 1 (page 4).

9 Page 8 (C) Plant root Lysis of surface microbes 1. Cut root into small pieces and place directly into ZR BashingBead Lysis Tubes (0.1 & 0.5 mm) with 750 µl of ZymoBIOMICS Lysis Buffer. 2. Lysis should be performed with a lower speed bead beating device (e.g. vortex adapter for 20 minutes) to avoid the host tissue contamination. 3. Continue to Step 3 (page 4) and proceed with the remaining protocol as written. Water/Air Samples 1. Filter samples using desired filter (not provided) prior to Step 1 (page 4). 2. Cut the filter into small pieces and place them inside the ZR BashingBead Lysis Tubes (0.1 & 0.5 mm), and add 750 µl of ZymoBIOMICS Lysis Solution. 3. Continue to Step 2 (page 4) and proceed with the remaining protocol as written. Lytic Enzymes Lytic enzymes, such as Lysozyme, Lysostaphin, MetaPolyzyme, etc. can be used with this kit using the following: (A) Enzymatic lysis followed by bead beating: 1. Perform enzymatic digestion under manufacturer s recommended conditions (temperature/time/concentration). Note: If sample is stored in DNA/RNA Shield, perform the following: a. Centrifuge sample at 10,000 x g for 1 minute. b. Transfer supernatant to a ZR BashingBead Lysis Tube (0.1 & 0.5 mm), to be used in Step 2, below. c. Re-suspend pellet in a buffer suitable for enzymatic treatment (ex. PBS or other isotonic solution). 2. Transfer the digestion mixture to a ZR BashingBead Lysis Tube (0.1 & 0.5 mm). 3. Add 750 µl ZymoBIOMICS Lysis Solution. Note: For samples in DNA/RNA Shield, raise to a final volume of 1 ml with DNA/RNA Shield. 4. Proceed to Step 2 (page 4) and continue with the remaining protocol as written. (B) Enzymatic lysis only (no bead beating): 1. Perform enzymatic digestion under manufacturer s recommended conditions (temperature/time/concentration). Note: If sample is stored in DNA/RNA Shield, perform the following: a. Centrifuge sample at 10,000 x g for 1 minute. b. Transfer supernatant to a clean microcentrifuge tube, to be used in Step 2. c. Re-suspend pellet in a buffer suitable for enzymatic treatment (ex. PBS or other isotonic solution). 2. Raise the volume of sample to 400 µl with ZymoBIOMICS Lysis Solution. 3. Continue to Step 4 (page 4) and proceed with the remaining proceed as written. Hair, Feather, and Nail Samples: 1. To 25 mg sample, add 90 µl Water, 90 µl Solid Tissue Buffer (Blue) (Cat. No. D ), 10 µl 1M DTT, and 10 µl Proteinase K (Cat. No. D ) in a microcentrifuge tube. 2. Mix thoroughly or vortex seconds and then incubate the tube at 55 º C overnight. 3. Transfer lysate to a ZR BashingBead Lysis Tube (0.1 & 0.5 mm) and then add 750 µl ZymoBIOMICS Lysis Solution. 4. Continue to Step 2 (page 4) and proceed with the remaining protocol as written.

10 Page 9 Tissue and Insect Samples Tissue and Insect samples can be processed three different ways, depending on the sample type and the equipment available. The recommendations are listed next to the options below: (A) Proteinase K - Tissue 1. Add up to 15 mg of tissue to a 1.5 ml microcentrifuge tube, then add a solution of 95 µl water, 95 µl Solid Tissue Buffer (Blue) (Cat. No. D ) and 10 µl Proteinase K (Cat. No. D ). Incubate for at least 1 hour at 55 C or until tissue clarifies (samples can be incubated overnight without affecting DNA quality). 2. Transfer digestion to a ZR BashingBead Lysis Tube (0.1 & 0.5 mm) and add 750 µl of ZymoBIOMICS Lysis Solution. 3. Proceed to Step 2 (page 4) and continue with the protocol as written. (B) Bead beating -Tissue and Insect 1. Add up to 15 mg of tissue/insect sample in a ZR BashingBead Lysis Tube (2.0 mm) (Cat. No. S ) with 750 µl of ZymoBIOMICS Lysis Solution. 2. Secure in a bead beater fitted with a 2 ml tube holder assembly and process at maximum speed for 5 minutes. Note: Processing time will vary based on sample input and bead beater. Times may be as little as 5 minutes when using high-speed cell disrupters (FastPrep -24) or as long as 20 minutes when using lower speeds (e.g., Disruptor Genie ). 3. Transfer the entire lysate to the ZR BashingBead Lysis Tube (0.1 & 0.5 mm), proceed to Step 2 (page 4), and continue with protocol as written. (C) Mortar & Pestle - Tissue and Insect 1. Homogenize up to 15 mg tissue/insect sample with a mortar and pestle while submersed in liquid nitrogen. 2. Transfer the entire sample into the ZR BashingBead Lysis Tube (0.1 & 0.5 mm) and add 750 µl of ZymoBIOMICS Lysis Solution. 3. Proceed to Step 2 (page 4) and continue with the protocol as written. Samples Collected with Swabs (A) Directly process swab 1. Directly break swab at breakpoint or cut the swab into a ZR BashingBead Lysis Tube (0.1 & 0.5 mm). 2. Proceed to Step 1 (page 4) and continue with the protocol as written. (B) Indirectly process swab 1. Vortex the swab in the ZR BashingBead Lysis Tube (0.1 & 0.5 mm) with 750 µl of ZymoBIOMICS Lysis Solution for 30 seconds to transfer the microbes into solution. 2. Remove the swab and proceed to bead beating in Step 2 (page 4). Figure 5. Phylum composition of a simulated microbial community when bead beating was performed with and without the presence of a Puritan HydraFlock sterile flocked collection device placed in a ZR BashingBead Lysis Tube and processed at maximum speed (6.5 m/s) for 5 minutes. The extracted DNA was then subjected to microbial composition profiling via 16S rrna gene targeted sequencing. Experiment was performed in technical duplicates

11 Page 10 Bacterial Endospore Lysis ZymoBIOMICS DNA Miniprep Kit is capable of effectively lysing bacterial endospores, and also achieves higher yield when compared to competition. Figure 6. DNA Extractions were performed using the ZymoBIOMICS DNA Kit and DNeasy PowerSoil with 6 x 10 8 B. subtilis CFU. DNeasy PowerSoil reovered 0.62 ng/µl DNA, while the ZymoBIOMICS DNA Kit was capable of recovering 9.67 ng/µl in a 50 µl elution volume. Extractions were performed in triplicate and quantified via Qubit. Urine (A) Pelleting cells from fresh/frozen urine 1. Pellet the bacterial cells by centrifuging the urine at 15,000 x g for 10 minutes. 2. Without disturbing the pellet, slowly decant or pipette out the supernatant, leaving behind µl of pellet. 3. Add ZymoBIOMICS Lysis Solution to a final volume of 800 µl and then transfer the mixture to a ZR BashingBead Lysis Tube (0.1 & 0.5 mm). Proceed to Step 2 (page 4) and continue with the protocol as written. (B) Pelleting cells from stabilized urine 1. Add 70 µl Urine Conditioning Buffer (Cat. No. D ) for every 1 ml of urine and mix well by vortexing. Note: Urine stabilized by the Urine Conditioning Buffer can be stored for up to 1 month at ambient temperature. When samples are ready to be processed, mix well by vortexing, and proceed to Step Centrifuge at 3,000 x g for 15 minutes. 3. Without disturbing the pellet, slowly decant or pipette out the supernatant, leaving behind µl of pellet. 4. Add ZymoBIOMICS Lysis Solution to a final volume of 800 µl and then transfer the mixture to a ZR BashingBead Lysis Tube (0.1 & 0.5 mm). Proceed to Step 2 (page 4) and continue with the protocol as written. Figure 7. Phylum composition of urine preserved in Urine Conditioning buffer (UCB ), which preserves the microbial composition of urine with simulated stool contamination for a month at room temperature. Urine with UCB added (Zymo Research, D ) was stored at room temperature and analyzed over a month period. At the indicated time points (0 Days, 2 weeks, and 1 month), DNA was extracted using the ZymoBIOMICS DNA Miniprep Kit. The extracted DNA was then subjected to microbial composition profiling via 16S rrna gene targeted sequencing. Experiment was performed in technical duplicates. 0 Day 2 Weeks 1 Month

12 Page 11 Appendix C Standardize Sample Preparation with ZymoBIOMICS Microbial Community Standards The ZymoBIOMICS Microbial Community Standard (Cat. No. D6300) is a mock microbial community of defined and well characterized composition making it the perfect control for all microbiome profiling and metagenomics analyses. It is ideal for assessing bias of DNA extraction methods since it contains three easy-to-lyse Gram-negative bacteria (e.g. Escherichia coli), five tough-to-lyse Gram-positive bacteria (e.g. Listeria monocytogenes), and two tough-to-lyse yeasts (e.g. Saccharomyces cerevisiae). Bead Beating Device Calibration Protocol: Zymo Research suggests calibrating bead beating devices with the ZymoBIOMICS Microbial Community Standard in order to ensure bias free microbial extraction. For Disruptor Genie, vortex adapters, and vortex lysis we suggest a time course ranging from minutes with the vortex at maximum speed. For high speed cell disruptors such as the MP FastPrep -24 we suggest a time course at maximum speed with a range of 3-10 minutes. The resulting DNA should be evaluated by quantifying DNA yield and changes in microbial profile at each time point. The bead beating time that yields a profile that closely matches the theoretical composition should become standard operating procedure for the bead beating device. ZymoBIOMICS Microbial Community DNA Standard (Cat. No. D6305) is a mixture of genomic DNA extracted from pure cultures of eight bacterial and two fungal strains. Genomic DNA from each culture was quantified before mixing. The ZymoBIOMICS Microbial Community Standard allows for assessment of bias from library preparation, sequencing, and bioinformatics analysis. It serves perfectly as a microbial standard for benchmarking the performance of microbiomics or metagenomics analyses, including those provided by a 3 rd party. Accurate composition for reliable use to evaluate shotgun seq. and 16S rrna seq. gdna by Shotgun Sequencing 16S Counts by 16S Sequencing Species GC % Gram Stain gdna Abun. (%) Pseudomonas aeruginosa Escherichia coli Salmonella enterica Lactobacillus fermentum Enterococcus faecalis Staphylococcus aureus Listeria monocytogenes Bacillus subtilis Saccharomyces cerevisiae 38.4 Yeast 2 Cryptococcus neoformans 48.2 Yeast 2 Figure 8. Characterization of the microbial composition of the two ZymoBIOMICS standards with shotgun metagenomic sequencing (left panel) and 16S rrna gene targeted sequencing (right panel). The measured composition of the two standards agrees with the theoretical/designed composition. DNA Standard represents ZymoBIOMICS Microbial Community DNA Standard (DNA version) and Microbial Standard represents ZymoBIOMICS Microbial Community Standard (cellular version). Genomic DNA composition by shotgun sequencing was calculated based on counting the amounts of raw reads mapped to each genome. 16S composition by 16S rrna gene targeted sequencing was calculated based on counting the amount of 16S raw reads mapped to each genomes.

13 Page 12 A) Use ZymoBIOMICS Microbial Standards for assessing GC-Bias in Shotgun Metagenomics B) Perfect for tracking PCR Chimera in 16S rrna Gene Sequencing Figure 9. A) Library preparation for shotgun metagenomic sequencing was performed in two different ways: one by supplier I and one by an in-house method. Shotgun sequencing was performed on Illumina MiSeq with paired-end sequencing (2 x 150 bp). Raw reads were mapped to the 10 microbial genomes to evaluate the potential effect of GC content on sequencing coverage. Normalized coverage was calculated by normalization by the average sequencing coverage of each genome B) PCR chimera increases with PCR cycle number in the library preparation process of 16S rrna gene targeted sequencing. 20 ng ZymoBIOMICS Microbial Community Standard was used a template. The PCR reaction was performed with ZymoBIOMICS PCR Premix and with primers that target v3-4 region of 16S rrna gene. Chimera rate in percentage was determined with Uchime and using the 16S rrna gene of the 8 bacterial strains in the standard as reference PCR. chimera sequences were defined as sequences resulted from the recombination/hybridization of different template sequences. Appendix D Troubleshooting: For Technical Assistance, please contact or tech@zymoresearch.com. Problem Possible Causes and Suggested Solutions Clean workspace, centrifuge, and pipettes with 10% bleach to routinely to avoid contamination. Background Contamination Use of kit in exposed environment without proper filtration. Check pipettes, pipette tips, microcentrifuge tubes, workspace, etc. for contamination. Make sure bags of columns and buffer bottles are properly sealed for storage. Use of these outside a clean room or hood can result in contamination.

14 Page 13 Lysis Methods When using a Disruptor Genie, vortex adapter, vortex, or similar processing times will vary. Suggested beat beating time is anywhere from 5-20 minutes. Calibrate bead beating times to your particular device and application by testing several different time points before using precious samples. (Suggested times to test: 10, 20, and 30 minutes.) See Appendix C for details. When using high-speed bead bashing devices (e.g. Bertin Percellys, MP FastPrep24) run max speed for 5 minutes to ensure unbiased lysis. Incomplete Debris Removal Low DNA Yield For high density samples, ensure lysate is centrifuged properly to pellet insoluble debris following bead beating. Ensure that none of the debris is transferred to the Zymo-Spin III-F Filter in the next step. Input If the lysate does not pass through the column or is extremely viscous, use less input material. Too much sample input can cause cellular debris to overload the column and insufficient flow Consult the Sample Input Table on Page 4 for information on your particular input limit based on sample. Binding Step Ensure that the ZymoBIOMICS DNA Binding Buffer is completely mixed with lysate before loading onto the column. Improperly mixed samples can lead to poor DNA recovery. Elution Procedure Ensure the ZymoBIOMICS DNase/RNase Free Water hydrates the matrix for at least 1 minute before centrifugation. To increase yields, heat the ZymoBIOMICS DNase/RNase Free Water to 60ºC before use. Additionally, users can reload the eluate onto the column matrix, incubate at room temperature for 3 minutes, and centrifuge again to increase yield without further dilution.

15 Page 14 Ordering Information Product Description Catalog No. Kit Size ZymoBIOMICS DNA Microprep Kit D preps. ZymoBIOMICS DNA Microprep Kit (Lysis Matrix Not Included) D preps. ZymoBIOMICS DNA Miniprep Kit D preps. ZymoBIOMICS DNA Miniprep Kit (Lysis Matrix Not Included) D preps. ZymoBIOMICS -96 DNA Kit (Includes BashingBead Lysis Rack) D4303 2x96 preps. ZymoBIOMICS - 96 DNA Kit (Includes BashingBead Lysis Tubes) D4309 2x96 preps. ZymoBIOMICS - 96 DNA Kit (Lysis Matrix Not Included) D4307 2x96 preps. ZymoBIOMICS -96 Magbead DNA Kit (Includes BashingBead Lysis Rack) D4302 2x96 preps. ZymoBIOMICS - 96 Magbead DNA Kit (Includes BashingBead Lysis Tubes) D4308 2x96 preps. ZymoBIOMICS - 96 Magbead DNA Kit (Lysis Matrix Not Included) D4306 2x96 preps. For Individual Sale Catalog No. Amount ZR BashingBead Lysis Tubes (0.1 & 0.5 mm) S ZymoBIOMICS Lysis Solution D ml ZymoBIOMICS DNA Binding Buffer D ml ZymoBIOMICS DNA Wash Buffer 1 D ml ZymoBIOMICS DNA Wash Buffer 2 D ml ZymoBIOMICS DNase/RNase Free Water D ml Zymo-Spin III-F Filters C OneStep PCR Inhibitor Removal Kit D Collection Tubes C C C ,000 Sample Collection Catalog No. Amount DNA/RNA Shield - Lysis Tube (Microbe) R DNA/RNA Shield Fecal Collection Tube R DNA/RNA Shield Swab and Collection Tube DNA/RNA Shield DNA/RNA Shield (2X concentrate) R1106 R1107 R R R R ml 250 ml 25 ml 125 ml ZymoBIOMICS, Zymo-Spin, and DNA/RNA Shield are trademarks of Zymo Research Corp. Disruptor Genie is a registered trademark of Scientific Industries, Inc. FastPrep is a registered trademark of Qbiogene, Inc. Illumnia MiSeq, Illumnia NexTera XT are trademarks or registered trademarks of Illumina Inc. AcroMetrix is a trademark of Thermo Fisher Scientific Inc. ZymoBIOMICS DNA Miniprep Kit is for research use only. ZymoBIOMICS DNA Miniprep Kit is not sold for use in diagnostic procedures. Reagents included with this kit are irritants. Follow the safety guidelines and rules enacted by your research institution or facility including the wearing of protective gloves and eye protection when using this kit.